umm if your keeping the stock head unit then i would look into a sound processor to clean up what it puts out then have it go into a small amp. this would be the ideal route to go.
something like this: http://www.crutchfield.com/S-UXz0laK...er-reviews-tab
or what would happen is amps have a high level input where you would connect the speaker wires right into and that's how it gets the signal.
amp : http://www.sonicelectronix.com/item_...-ONX2.100.html